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BaderLab / EnrichmentMapApp

The EnrichmentMap Cytoscape App allows you to visualize the results of gene-set enrichment as a network.
http://apps.cytoscape.org/apps/enrichmentmap
GNU Lesser General Public License v2.1
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Enrichment map error: "Failed: None of the gene sets have passed the filter" #358

Closed giuseppedelnapalle closed 5 years ago

giuseppedelnapalle commented 5 years ago

Hi all,

I am looking for help to fix the problem of failing to build enrichment map. I tried to do it after doing GSEA, but I got the error shown below.

Unable to create Enrichment Map:Internal Server ErrorResponseEntityProxy

There's no error throughout GSEA, and I built the enrichment map successfully with the example files from this tutorial. So the problem was likely to be caused by the input files. Additionally, error could not be avoided either using Cytoscape 3.6.1 or 3.7.0. The issue was initially posted at GSEA help forum, so please follow the link for more details.

Software information: OS: Windows 10 GSEA: 3.0 (build 0160) Cytoscape: 3.7.0 Java: 1.8.0_191

Thanks!

risserlin commented 5 years ago

I think that the issue relates to the title of the bug "none of the gene sets have passed filter". Change the p-value and FDR threshold to something really lax like p.value --> 1.0 and FDR --> 0.5 and re-try creating the network. Do you get the same issue? screen shot 2018-12-13 at 10 43 03 am

giuseppedelnapalle commented 5 years ago

Thanks, you are right. The parameters I used as recommended (p-value<0.05 & FDR <0.25) were too stringent for my data.

ernstki commented 5 years ago

gsea_cytoscape_error_message+shadow

@mikekucera This is an extremely user-unfriendly way of saying "None of the gene sets have passed the filter. Try relaxing the gene set filter parameters." You only discover that's the actual problem if you manage to figure out how to look at the GSEA application log.

Is this a GSEA bug, or an EnrichmentMap bug, or a Cytoscape bug? Someone needs to throw the poor user a bone here, because this issue comes up again and again in Internet forums.

mikekucera commented 5 years ago

Looks like a problem in GSEA desktop. Its not properly displaying the error message returned by EnrichmentMap.

ernstki commented 5 years ago

@mikekucera Wicked. Thanks for opening a pull request for it. :)